VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue May 26 2020 - 11:52:02 CDT

Bonds made in molefacture will only propagate to other environments that
actually care about the connectivities defined in your structure file.
Psfgen emphatically does not -- it will use the connectivities from the
topology file, so to make the bonds that you want, you need to use patch
statements (as Josh suggested). To fix the 'unparameterized component'
error, please be sure that the topology files that you actually have loaded
contain a residue with residue/atom names exactly matching your molecule of
interest. If you used a bunch of topology files for CHARMM-GUI, you need to
make sure that you're using the same ones in autopsf.
Best,
Peter

On Tue, May 26, 2020 at 12:42 PM Josh Vermaas <joshua.vermaas_at_gmail.com>
wrote:

> Whats the residue name in the topology files CHARMM-GUI provided, and does
> it match what is in the input structure? That is how psfgen/autopsf does
> the matching, and if that is incorrect, Autopsf will ignore the parts that
> aren't parameterized. I'm not entirely sure how the molefacture part screws
> around with this, but I've always done it the old-fashioned patching way.
> -Josh
>
> On Tue, May 26, 2020 at 8:31 AM Hélder Bandarra Tavares <
> H.D.BandarraTavares_at_tudelft.nl> wrote:
>
>> I'm trying to bind a molecule (mostly composed of PEG chains) to
>> Hemolysin. I have the .pdb and .psf files of both. To do so, I placed the
>> molecule close to the residue I want to link it to and created a bond using
>> Molefacture, and now I wanted to generate a .psf file to run a MD
>> minimization/equilibration afterwards with NAMD. However, using Autopsf I
>> get the following message: "Autopsf has detected 1 unparametrized
>> components", and this component is the molecule I want to link. It is worth
>> noting that that molecule has no non-standard atoms and that I loaded the
>> topology files provided by CHARMM-GUI for this molecule.
>>
>>
>> What can I do to generate the .psf file? Is there other way to do so?
>>
>>
>> Thank you in advance,
>>
>> Hélder Tavares
>>
>>
>>
>>